A new method for the fabrication of periodic CNT arrays was developed in this study, which involves the use of the inverse nano-sphere lithography (INSL) process. Mo of a honeycomb pattern, acting as a catalyst-poisoning layer, was produced by the nano-sphere lithography (NSL) process; the Mo poisoned the catalyst and prevented CNT growth where deposited, and as a result, a periodic CNT pattern was obtained. Using this method, the uniformity of the CNT array can be improved by preventing the negative effect of arrangement defects in self-assembled monolayers. The size and the period of the CNT array can be adjusted by careful selection of the polystyrene (PS) sphere diameter. X-ray photoelectron spectroscope (XPS) analysis revealed that the Co catalyst was ineffective on the areas of Mo deposition due to the diffusion of Co into the Mo layer.